Research workbench
Crystal structure of thioredoxin reductase from brugia malayi
Analyse Crystal structure of thioredoxin reductase from brugia malayi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P0X
- Type
- protein
- Length
- 1,707 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaredoxin domain-containing protein
- UniProt
- A0A0J9XPH7
- Ligands
- FAD, NA, CL
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaredoxin domain-containing protein | protein | 576 | 37% helix, 25% strand | A0A0J9XPH7 |
| B | Glutaredoxin domain-containing protein | protein | 581 | 37% helix, 25% strand | A0A0J9XPH7 |
| C | Glutaredoxin domain-containing protein | protein | 550 | 37% helix, 22% strand | A0A0J9XPH7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.81 | 0.83 | 118 | FAD, MPD |
| 2 | 812 | 0.81 | 0.84 | 110 | FAD, MPD |
| 3 | 1086 | 0.79 | 0.81 | 130 | FAD |
| 4 | 124 | 0.78 | 0.97 | 21 | empty |
| 5 | 113 | 0.78 | 0.97 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3917 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 224 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 7P0X · Crystal structure of Thioredoxin reductase from Brugia Malayi · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A0J9XPH7
- Elsewhere: RCSB PDB 7P0X · PDBe 7P0X · UniProt A0A0J9XPH7
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